Employing the tools ClustalW, RNAalifold, RNAfold and RNAforester, this pipeline can improve structural conservation
of RNA sequences within the twilight zone of 30-60% sequence identity. After constructing a consensus structure by
alignment folding, plan AC* abandons the original sequence alignment, refolds structures individually, but restricted
by the consensus, aligns the structures (irrespective of sequence) by a pure structure alignment method, and derives
an improved sequence alignment from the alignment of structures, to be re-submitted to alignment folding, etc...

Perl Implementation of Plan AC*, needs BioPerl to be installed on your System.